Index _ | A | B | C | D | E | F | G | I | K | L | M | N | P | R | S | T | U | V | W | Z _ __dir__() (in module spatiomic) __version__ (in module spatiomic) A agglomerative (class in spatiomic.cluster) anndata_from_array() (in module spatiomic.data) apply_homography() (spatiomic.process.register static method) apply_optical_flow() (spatiomic.process.register static method) apply_shift() (spatiomic.process.register static method) autocorrelation (class in spatiomic.spatial) B batch_size (spatiomic.dimension.pca attribute) bivariate_correlation (class in spatiomic.spatial) C clip (class in spatiomic.process) cluster_contributor_histogram() (in module spatiomic.plot) cluster_contributors() (in module spatiomic.plot) cluster_count (spatiomic.cluster.agglomerative attribute) (spatiomic.cluster.kmeans attribute) cluster_image() (in module spatiomic.plot) cluster_legend() (in module spatiomic.plot) cluster_location() (in module spatiomic.plot) cluster_scatter() (in module spatiomic.plot) cluster_selection() (in module spatiomic.plot) colormap() (in module spatiomic.plot) connectivity (spatiomic.cluster.agglomerative attribute) connectivity_graph() (in module spatiomic.plot) count_clusters() (in module spatiomic.tool) create() (spatiomic.neighbor.knn_graph class method) (spatiomic.neighbor.snn_graph class method) D dimension_count (spatiomic.dimension.pca attribute) (spatiomic.dimension.tsne attribute) (spatiomic.dimension.umap attribute) distance_metric (spatiomic.cluster.agglomerative attribute) (spatiomic.dimension.tsne attribute) (spatiomic.dimension.umap attribute) distance_min (spatiomic.dimension.umap attribute) E estimator (spatiomic.process.normalize attribute) F fill_value (spatiomic.process.clip attribute) fit() (spatiomic.cluster.som method) (spatiomic.dimension.pca method) (spatiomic.dimension.som method) (spatiomic.dimension.umap method) (spatiomic.process.clip method) (spatiomic.process.normalize method) (spatiomic.process.zscore method) fit_predict() (spatiomic.cluster.agglomerative method) (spatiomic.cluster.kmeans method) (spatiomic.cluster.som method) (spatiomic.dimension.som method) fit_transform() (spatiomic.data.subsample static method) (spatiomic.dimension.pca method) (spatiomic.dimension.tsne method) (spatiomic.dimension.umap method) (spatiomic.process.clip method) (spatiomic.process.log1p method) (spatiomic.process.normalize method) (spatiomic.process.zscore method) fitted (spatiomic.process.clip attribute) (spatiomic.process.normalize attribute) G get_config() (spatiomic.cluster.som method) (spatiomic.dimension.som method) get_czi_image_channels() (spatiomic.data.read static method) get_edges() (spatiomic.neighbor.knn_graph static method) get_explained_variance_ratio() (spatiomic.dimension.pca method) get_homography() (spatiomic.process.register static method) get_loadings() (spatiomic.dimension.pca method) get_nodes() (spatiomic.cluster.som method) (spatiomic.dimension.som method) get_optical_flow() (spatiomic.process.register static method) get_phase_shift() (spatiomic.process.register static method) get_quantization_error() (spatiomic.cluster.som method) (spatiomic.dimension.som method) get_shared_neighbors() (spatiomic.neighbor.snn_graph static method) get_shift() (spatiomic.process.register class method) get_ssim() (spatiomic.process.register static method) get_stats() (in module spatiomic.tool) graph (spatiomic.cluster.leiden attribute) I init (spatiomic.cluster.kmeans attribute) inverse_transform() (spatiomic.process.log1p method) iteration_count (spatiomic.cluster.kmeans attribute) (spatiomic.dimension.tsne attribute) iteration_count_without_progress (spatiomic.dimension.tsne attribute) K kmeans (class in spatiomic.cluster) knn_graph (class in spatiomic.neighbor) L label() (spatiomic.cluster.som method) (spatiomic.dimension.som method) learning_rate (spatiomic.dimension.tsne attribute) leiden (class in spatiomic.cluster) load() (spatiomic.cluster.som method) (spatiomic.dimension.som method) (spatiomic.process.clip class method) (spatiomic.process.normalize class method) (spatiomic.process.zscore class method) local_autocorrelation (class in spatiomic.spatial) local_heteroskedasticity (class in spatiomic.spatial) log1p (class in spatiomic.process) M marker_expression() (in module spatiomic.plot) max_value (spatiomic.process.clip attribute) (spatiomic.process.normalize attribute) mean (spatiomic.process.zscore attribute) mean_cluster_intensity() (in module spatiomic.tool) method (spatiomic.process.clip attribute) min_value (spatiomic.process.clip attribute) (spatiomic.process.normalize attribute) module spatiomic spatiomic.cluster spatiomic.data spatiomic.dimension spatiomic.neighbor spatiomic.plot spatiomic.process spatiomic.spatial spatiomic.tool N neighbor_count (spatiomic.dimension.umap attribute) neighborhood_offset() (in module spatiomic.spatial) normalize (class in spatiomic.process) P pca (class in spatiomic.dimension) percentile_max (spatiomic.process.clip attribute) percentile_max_absolute (spatiomic.process.clip attribute) percentile_min (spatiomic.process.clip attribute) percentile_min_absolute (spatiomic.process.clip attribute) perplexity (spatiomic.dimension.tsne attribute) predict() (spatiomic.cluster.leiden method) (spatiomic.cluster.som method) (spatiomic.dimension.som method) (spatiomic.spatial.autocorrelation method) (spatiomic.spatial.bivariate_correlation method) (spatiomic.spatial.local_autocorrelation class method) (spatiomic.spatial.local_heteroskedasticity class method) R read (class in spatiomic.data) read_czi() (spatiomic.data.read class method) read_lif() (spatiomic.data.read static method) read_tiff() (spatiomic.data.read static method) register (class in spatiomic.process) registration_similarity() (in module spatiomic.plot) registration_slope() (in module spatiomic.plot) run_count (spatiomic.cluster.kmeans attribute) S save() (spatiomic.cluster.som method) (spatiomic.dimension.som method) (spatiomic.process.clip method) (spatiomic.process.normalize method) (spatiomic.process.zscore method) save_cluster_image() (in module spatiomic.plot) save_cluster_selection() (in module spatiomic.plot) seed (spatiomic.cluster.kmeans attribute) (spatiomic.dimension.tsne attribute) (spatiomic.dimension.umap attribute) set_config() (spatiomic.cluster.som method) (spatiomic.dimension.som method) set_estimator() (spatiomic.cluster.agglomerative method) (spatiomic.cluster.kmeans method) (spatiomic.dimension.pca method) (spatiomic.dimension.tsne method) (spatiomic.dimension.umap method) set_estimators() (spatiomic.cluster.som method) (spatiomic.dimension.som method) set_nodes() (spatiomic.cluster.som method) (spatiomic.dimension.som method) snn_graph (class in spatiomic.neighbor) som (class in spatiomic.cluster) (class in spatiomic.dimension) som_clusters() (in module spatiomic.plot) som_distance() (in module spatiomic.plot) som_marker_expression() (in module spatiomic.plot) spatial_graph() (in module spatiomic.plot) spatial_weights() (in module spatiomic.spatial) spatiomic module spatiomic.cluster module spatiomic.data module spatiomic.dimension module spatiomic.neighbor module spatiomic.plot module spatiomic.process module spatiomic.spatial module spatiomic.tool module split_multi_image_lif() (spatiomic.data.read static method) spread (spatiomic.dimension.umap attribute) std (spatiomic.process.zscore attribute) subsample (class in spatiomic.data) subset() (in module spatiomic.data) T tolerance (spatiomic.cluster.kmeans attribute) transform() (spatiomic.dimension.pca method) (spatiomic.dimension.umap method) (spatiomic.process.clip method) (spatiomic.process.log1p method) (spatiomic.process.normalize method) (spatiomic.process.zscore method) tsne (class in spatiomic.dimension) U umap (class in spatiomic.dimension) use_gpu (spatiomic.cluster.agglomerative attribute) (spatiomic.cluster.kmeans attribute) (spatiomic.cluster.som attribute) (spatiomic.dimension.pca attribute) (spatiomic.dimension.som attribute) (spatiomic.dimension.tsne attribute) (spatiomic.dimension.umap attribute) (spatiomic.process.normalize attribute) (spatiomic.process.zscore attribute) V vicinity_composition() (in module spatiomic.spatial) vicinity_graph() (in module spatiomic.spatial) volcano() (in module spatiomic.plot) W weigh_by_explained_variance_ratio() (spatiomic.dimension.pca method) Z zscore (class in spatiomic.process)